My two cents, why not delegating some skills to officers dedicated to specific aspects of the game like:
- Engeneer officer, for everything regarding, repair, salvage, ship recovery, fuel consuption, ...
- Scientific officer, for surveying, mainly
In my view our character is an admiral or a fleet commander, so there is surely a team of officer under his command that takes responsibility for some specific duty. Our character could have a few skills in those area, just to add a small bonus to the skill of the dedicated officer.
Those officers can gain skills through action, but also through training in academy, for example.
Another aspect could be to change the mechanic of survey. Instead of requirering a certain level to be able to survey, it could be better to have a certain level of failure at that task. When failing, a part of the machinery and/or crew is lost. That allows to perform survey on any kind of planet, even at low level, but, will make it harder to players that don't concentrate on that kind of stuff, without preventing them from performing that kind of tasks.